TCGA2STAT statistics

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Protocols

TCGA2STAT specifications

Information


Unique identifier OMICS_10650
Name TCGA2STAT
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.2
Stability Stable
Requirements
parallel, knitr, CNTools, XML, R(≥3.0.0)
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Ying-Wooi Wan

Publication for TCGA2STAT

TCGA2STAT citations

 (8)
call_split

Association between expression of random gene sets and survival is evident in multiple cancer types and may be explained by sub classification

2018
PLoS Comput Biol
PMCID: 5839591
PMID: 29470520
DOI: 10.1371/journal.pcbi.1006026
call_split See protocol

[…] We downloaded TCGA data from the TCGA data matrix on November 30, 2015 using the TCGA2STAT R package []; This gave us a total of 34 RNAseq expression datasets with their adjoining survival and clinical information. We used the level 3 data normalized using RSEM. We used the datase […]

library_books

Improved high dimensional prediction with Random Forests by the use of co data

2017
BMC Bioinformatics
PMCID: 5745983
PMID: 29281963
DOI: 10.1186/s12859-017-1993-1

[…] A RNASeqv2 profiles of head-and-neck squamous cell carcinomas (HNSCC), which were downloaded together with the matching normalized DNA copy number co-data from Broad GDAC Firehose using the R package TCGA2STAT. Of the 279 patients described in [], we used the subset of 133 patients that had HPV-negative tumors in the oral cavity. Of these patients, 76 presented a LNM and 57 did not.To enhance the […]

library_books

Villi specific Gene Expression Reveals Novel Prognostic Biomarkers in Multiple Human Cancers

2017
PMCID: 5604211
PMID: 28928868
DOI: 10.7150/jca.19787

[…] We used the R package “TCGA2STAT” to download the RNA-Seq data and clinical data of patients representing 32 cancer types from The Cancer Genome Atlas (TCGA) database. For RNA-Seq data, we downloaded the RNAseqV2 data for e […]

library_books

A novel signature for stratifying the molecular heterogeneity of the tissue infiltrating T cell receptor repertoire reflects gastric cancer prognosis

2017
Sci Rep
PMCID: 5552765
PMID: 28798410
DOI: 10.1038/s41598-017-08289-z

[…] the log-rank test using the R package “survival”. The RNA-seq data and corresponding clinical information, which were available for 388 GC samples, were downloaded from TCGA database using R Package “TCGA2STAT”. […]

library_books

Integrated transcriptomic analysis of distance related field cancerization in rectal cancer patients

2017
Oncotarget
PMCID: 5617410
PMID: 28977850
DOI: 10.18632/oncotarget.17864

[…] TCGA CRC RNA sequencing data used for the survival analysis were accessed using the R package “TCGA2STAT” []. We calculated 5-year overall survival for the 7-gene signature and for each single gene using data from the TCGA CRC dataset. Hierarchical clustering of the expression of the 7 genes di […]

library_books

Comprehensive analysis of The Cancer Genome Atlas reveals a unique gene and non coding RNA signature of fibrolamellar carcinoma

2017
Sci Rep
PMCID: 5356346
PMID: 28304380
DOI: 10.1038/srep44653

[…] tal and from the Cancer Digital Slide Archive. Liver histology was reviewed independently by two gastrointestinal pathologists (KGG, MST). Ages of patients were obtained from TCGA using the R package TCGA2STAT. […]

Citations

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TCGA2STAT institution(s)
Computational and Integrative Biomedical Research Center, Baylor College of Medicine, Houston, TX, USA

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